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- PDB-1qfh: DIMERIZATION OF GELATION FACTOR FROM DICTYOSTELIUM DISCOIDEUM: CR... -

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Basic information

Entry
Database: PDB / ID: 1qfh
TitleDIMERIZATION OF GELATION FACTOR FROM DICTYOSTELIUM DISCOIDEUM: CRYSTAL STRUCTURE OF ROD DOMAINS 5 AND 6
ComponentsPROTEIN (GELATION FACTOR)
KeywordsACTIN BINDING PROTEIN / IMMUNOGLOBULIN / GELATION FACTOR / ABP-120
Function / homology
Function and homology information


regulation of pseudopodium assembly / anterior cell cortex / Cell-extracellular matrix interactions / pseudopodium assembly / ISG15 antiviral mechanism / Platelet degranulation / sorocarp development / posterior cell cortex / chemotaxis to cAMP / lateral cell cortex ...regulation of pseudopodium assembly / anterior cell cortex / Cell-extracellular matrix interactions / pseudopodium assembly / ISG15 antiviral mechanism / Platelet degranulation / sorocarp development / posterior cell cortex / chemotaxis to cAMP / lateral cell cortex / phototaxis / macropinocytic cup / RHO GTPases activate PAKs / protein kinase B binding / actin crosslink formation / thermotaxis / hyperosmotic response / mitogen-activated protein kinase binding / lamellipodium assembly / cortical actin cytoskeleton / cell leading edge / pseudopodium / phagocytic cup / phagocytosis / response to cAMP / extracellular matrix / cell motility / small GTPase binding / actin filament binding / cell migration / cell cortex / actin cytoskeleton organization / plasma membrane / cytoplasm
Similarity search - Function
Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain ...Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsMccoy, A.J. / Fucini, P. / Noegel, A.A. / Stewart, M.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: Structural basis for dimerization of the Dictyostelium gelation factor (ABP120) rod.
Authors: McCoy, A.J. / Fucini, P. / Noegel, A.A. / Stewart, M.
#1: Journal: J.Struct.Biol. / Year: 1997
Title: Crystallization and preliminary X-Ray diffraction characterization of a dimerizing fragment of the rod domain of the Dictyostelium gelation factor (ABP-120).
Authors: Fucini, P. / McCoy, A.J. / Gomez-Ortiz, M. / Schleicher, M. / Noegel, A.A. / Stewart, M.
History
DepositionApr 11, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 27, 2019Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (GELATION FACTOR)
B: PROTEIN (GELATION FACTOR)


Theoretical massNumber of molelcules
Total (without water)44,7112
Polymers44,7112
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-13 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.448, 103.150, 124.361
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.64641, -0.680864, 0.344352), (-0.663308, -0.724509, -0.187375), (0.377063, -0.107291, -0.919952)12.968, 33.09, 2.675
2given(0.606333, -0.678262, 0.415115), (-0.700719, -0.702516, -0.124355), (0.375971, -0.215478, -0.90123)14.929, 33.123, 0.304

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Components

#1: Protein PROTEIN (GELATION FACTOR) / ACTIN BINDING PROTEIN 120 / Dictyostelium filamin / ddFLN


Mass: 22355.594 Da / Num. of mol.: 2 / Fragment: ROD DOMAINS 5 AMD 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: P13466
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.2 / Details: 30% PEG 1000, 0.1M TRIS_HCL PH 7.2, 25% GLYCEROL
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.6 mg/mlprotein11
220 mMpotassium phosphate12
3100 mM12NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.88
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 2.2→26.23 Å / Num. obs: 82513 / % possible obs: 98 % / Redundancy: 2.9 % / Biso Wilson estimate: 29.87 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 8.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.091 / Mean I/σ(I) obs: 6.9 / % possible all: 97.6
Reflection
*PLUS
Num. obs: 28551 / % possible obs: 98 % / Num. measured all: 82513
Reflection shell
*PLUS
% possible obs: 97.6 % / Num. unique obs: 4076 / Num. measured obs: 11993

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→26.63 Å / SU B: 5.42051 / SU ML: 0.14239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24148 / ESU R Free: 0.20983
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1442 5 %RANDOM
Rwork0.2216 ---
obs0.2192 28503 98 %-
Displacement parametersBiso mean: 42.59 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 0 237 3337
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.018
X-RAY DIFFRACTIONp_angle_d0.0190.019
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.713
X-RAY DIFFRACTIONp_mcangle_it2.4945
X-RAY DIFFRACTIONp_scbond_it3.0354
X-RAY DIFFRACTIONp_scangle_it4.3126
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1280.15
X-RAY DIFFRACTIONp_singtor_nbd00.05
X-RAY DIFFRACTIONp_multtor_nbd00.05
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.0610.05
X-RAY DIFFRACTIONp_planar_tor3.77
X-RAY DIFFRACTIONp_staggered_tor13.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor1420
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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